Try to create a new profile, then exit the game and copy the save from old profile to the new one, chances are it will load it. If it doesn't, you can temporarily revert to the old version to finish the game:Right-click on the game in Steam library, choose Properties, then select English language and OldVersion build from the Beta tab. Steam will download old files. Now navigate to C:\Program Files (x86)\Steam\steamapps\common\fantasy wars and rename fw.exe to FantasyWars.exe to be able to launch the old version of the game so you could finish it. Hope this helps.

Creating a new profile didn't seem to help; I still only see "fantasy wars\Profiles\Profile.01" where I was expecting a "Profile.02" to show up. I even started the first mission and saved, hoping to force the game to create a new "valid" directory for me to copy saves to, but it didn't (wonder where that save went).

Reverting to the old version did fix the problem. However, now I'm sad that, even after beating the game, I won't be able to easily come back to my old saves, and that I have to finish the game without all the new pathing goodies! But alas, glad I can finish now. Cheers.

Ah, i see now what the problem is :) New version of the game saves its progress into your Documents folder instead of installation folder. You can try to copy your existing Profile.01 from game folder to Documents\Fantasy Wars\Profiles and update the game again.